Department of Molecular Simulations of Polymers

Publications

Publications:
2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | Histogram IF

Publications 2017

ABC Chapters in scientific monographs published abroad
  1. RAČKO, Dušan - BENEDETTI, Fabrizio - DORIER, Julien - BURNIER, Yannis - STASIAK, Andrzej. Molecular dynamics simulation of supercoiled, knotted, and catenated DNA molecules, including modeling of action of DNA gyrase. In The Bacterial Nucleoid: Methods and Protocols. - Springer Science+Business Media LLC, 2017, vol. 1624, chapter. 24, P. 339-372. ISBN 978-1-4939-7098-8. Typ: ABC
ADCA Scientific papers in foreign journals registered in Current Contents Connect with IF (impacted)
  1. BENEDETTI, Fabrizio - RAČKO, Dušan - DORIER, Julien - BURNIER, Yannis - STASIAK, Andrzej. Transcription-induced supercoiling explains formationof self-interacting chromatin domains in S. pombe. In Nucleic acids research, 2017, vol. 45, no. 17, p. 9850-9859. (10.162 - IF2016). ISSN 0305-1048. Typ: ADCA
  2. BENKOVÁ, Zuzana - RIŠPANOVÁ, Lucia - CIFRA, Peter. Effect of chain stiffness for semiflexible macromolecules in array of cylindrical nanoposts. In Journal of Chemical Physics, 2017, vol.147, art.no. 134907. (2.965 - IF2016). (2017 - Current Contents, WOS, SCOPUS). ISSN 0021-9606. Typ: ADCA
  3. BENKOVÁ, Zuzana - RIŠPANOVÁ, Lucia - CIFRA, Peter. Structural behavior of a semiflexible polymer chain in an array of nanoposts. In Polymers : Open Access Polymer Science Journal, 2017, vol. 9, art. no. 313. (3.364 - IF2016). ISSN 2073-4360. Dostupné na internete: <www.mdpi.com/journals/polymers>. Typ: ADCA

Publications 2016

ADCA Scientific papers in foreign journals registered in Current Contents Connect with IF (impacted)
  1. BENKOVÁ, Zuzana - NÁMER, Pavol - CIFRA, Peter. Comparison of a stripe and slab confinement for ring and linear macromolecules in nanochannel. In Soft Matter, 2016, vol. 12, p. 8425-8439. (3.798 - IF2015). (2016 - Current Contents). ISSN 1744-683X. Typ: ADCA
  2. BHANDARY, Debdip - BENKOVÁ, Zuzana - CORDEIRO, M. Natália D. S. - SINGH, Jayant K. Molecular dynamics study of wetting behavior of grafted thermo-responsive PNIPAAm brushes. In Soft Matter, 2016, vol. 12, p. 3093-3102. (3.798 - IF2015). (2016 - Current Contents). ISSN 1744-683X. Typ: ADCA
  3. RAWDON, Eric J. - DORIER, Julien - RAČKO, Dušan - MILLETT, Kenneth C. - STASIAK, Andrzej. How topoisomerase IV can efficiently unknot and decatenate negatively supercoiled DNA molecules without causing their torsional relaxation. In Nucleic acids research, 2016, vol. 44, no. 10, p. 4528-4538. (9.202 - IF2015). (2016 - Current Contents). ISSN 0305-1048. Typ: ADCA

Publications 2015

ADCA Scientific papers in foreign journals registered in Current Contents Connect with IF (impacted)
  1. BENEDETTI, Fabrizio - JAPARIDZE, Aleksandre - DORIER, Julien - RAČKO, Dušan - KWAPICH, Robert - BURNIER, Yannis - DIETLER, Giovanni - STASIAK, Andrzej. Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling. In Nucleic acids research, 2015, vol. 43, no. 4, p. 2390-2399. (9.112 - IF2014). (2015 - Current Contents). ISSN 0305-1048. Typ: ADCA
  2. BENKOVÁ, Zuzana - CORDEIRO, M. Natalia D. S. Molecular dynamics simulations of poly(ethylene oxide) grafted onto silica immersed in melt of homopolymers. In Langmuir, 2015, vol. 31, p. 10254-10264. (4.457 - IF2014). (2015 - Current Contents). ISSN 0743-7463. Typ: ADCA
  3. BENKOVÁ, Zuzana - NÁMER, Pavol - CIFRA, Peter. Stripe to slab confinement for the linearization of macromolecules in nanochannels. In Soft Matter, 2015, vol. 11, p. 2279-2289. (4.029 - IF2014). (2015 - Current Contents). ISSN 1744-683X. Typ: ADCA
  4. PALENČÁR, Peter - BLEHA, Tomáš. Bending and kinking in helical polymers. In Journal of Polymer Science. Part B.Polymer Physics, 2015, vol. 53, p. 1345-1357. (3.830 - IF2014). (2015 - Current Contents). ISSN 0887-6266. Typ: ADCA
  5. PLAŠIENKA, Dušan - CIFRA, Peter - MARTOŇÁK, Roman. Structural transformation between long and short-chain form of liquid sulfur from ab initio molecular dynamics. In Journal of Chemical Physics, 2015, vol. 142, art. no. 154502. (2.952 - IF2014). (2015 - Current Contents). ISSN 0021-9606. Typ: ADCA
  6. RAČKO, Dušan - BENEDETTI, Fabrizio - DORIER, Julien - BURNIER, Yannis - STASIAK, Andrzej. Generation of supercoils in nicked and grapped DNA drives DNA unknotting and postreplicative decatenation. In Nucleic acids research, 2015, vol. 43, no. 15, p. 7229-7236. (9.112 - IF2014). (2015 - Current Contents). ISSN 0305-1048. Typ: ADCA
  7. RAČKO, Dušan - CIFRA, Peter. Arm retraction and escape transition in semi-flexible star polymer under cylindrical confinement. In Journal of molecular modeling, 2015, vol. 21, art.no. 186. (1.736 - IF2014). (2015 - Current Contents). ISSN 1610-2940. Typ: ADCA
ADMB Scientific papers in foreign non-impacted journals registered in Web of Sciences or Scopus
  1. CZANIKOVÁ, Klaudia - KRUPA, Igor - RAČKO, Dušan - ŠMATKO, Vasilij - CAMPO, Eva M. - PAWLOVA, Eva - OMASTOVÁ, Mária. In situ electron microscopy of Braille microsystems: photoactuation of ethylene vinyl acetate/carbon nanotube composites. In Materials Research Express, 2015, vol. 2, art.no. 025601. (2015 - SCOPUS). ISSN 2053-1591. Typ: ADMB

Publications 2014

ADCA Scientific papers in foreign journals registered in Current Contents Connect with IF (impacted)
  1. PALENČÁR, Peter - BLEHA, Tomáš. Buckling transition in long alpha-helices. In Journal of Chemical Physics, 2014, vol. 141, 174901 - 12 p. (3.122 - IF2013). (2014 - Current Contents). ISSN 0021-9606. Typ: ADCA
  2. RAČKO, Dušan. The free volume of condensed phases confined in a nanopore as seen by computer simulations and compared to PALS. In Acta Physica Polonica A, 2014, vol. 125, no. 3, p. 785-788. (0.604 - IF2013). (2014 - Current Contents, WOS, SCOPUS). ISSN 1898-794X. Typ: ADCA

Publications 2013

ADCA Scientific papers in foreign journals registered in Current Contents Connect with IF (impacted)
  1. BENKOVÁ, Zuzana - CIFRA, Peter. Comparison of linear and ring DNA macromolecules moderately and strongly confined in nanochannels. In Biochemical society transactions, 2013, vol. 41, p.625 -629. (2.587 - IF2012). (2013 - Current Contents). ISSN 0300-5127. Typ: ADCA
  2. CZANIKOVÁ, Klaudia - TORRAS, Núria - ESTEVE, Jaume - KRUPA, Igor - KASÁK, Peter - PAVLOVA, Ewa - RAČKO, Dušan - CHODÁK, Ivan - OMASTOVÁ, Mária. Nanocomposite photoactuators based on an ethylene vinyl acetate copolymer filled with carbon nanotubes. In Sensors and Actuators B-Chemical, 2013, vol. 186, p. 701 - 710. (3.535 - IF2012). (2013 - Current Contents). ISSN 0925-4005. Typ: ADCA
  3. DANKO, Martin - ANDICSOVÁ, Anita - HRDLOVIČ, Pavol - RAČKO, Dušan - VÉGH, Daniel. Spectral characteristics of carbonyl substituted 2,2´-bithiophenes in polymer matrices and low polar solvents. In Photochemical and Photobiological Sciences, 2013, vol. 12, p. 1210 - 1219. (2.923 - IF2012). (2013 - Current Contents). ISSN 1474-905X. Typ: ADCA
  4. PALENČÁR, Peter - BLEHA, Tomáš. Folding of alpha-helices into bundles in long polyalanines. In Computational and Theoretical Chemistry, 2013, vol. 1006, p. 62- 69. ISSN 2210-271X. Typ: ADCA
  5. PALENČÁR, Peter - BLEHA, Tomáš. Gas-phase compaction of helical polymers. In Polymer : the International Journal for the Science and Technology of Polymers, 2013, vol. 54, p. 4955 - 4962. (3.379 - IF2012). (2013 - Current Contents). ISSN 0032-3861. Typ: ADCA
  6. RAČKO, Dušan - CIFRA, Peter. Segregation of semiflexible macromolecules in nanochannel. In Journal of Chemical Physics, 2013, vol. 138, art.no. 184904. (3.164 - IF2012). (2013 - Current Contents). ISSN 0021-9606. Typ: ADCA
ADMB Scientific papers in foreign non-impacted journals registered in Web of Sciences or Scopus
  1. RAČKO, Dušan - KRIŠTIAK, Jozef. The free volume dynamics. In Materials Science Forum, 2013, vol. 733, p. 33 - 37. (2013 - WOS, SCOPUS). ISSN 0255-5476. Typ: ADMB
  2. RAČKO, Dušan. On the relatioship of the relative intensity I3 and a cavity number as obtained from computer simulations. In Materials Science Forum, 2013, vol. 733, p. 183-189. (2013 - WOS, SCOPUS). ISSN 0255-5476. Typ: ADMB

Publications 2012

ADCA Scientific papers in foreign journals registered in Current Contents Connect with IF (impacted)
  1. BENKOVÁ, Zuzana - CIFRA, Peter. Simulation of semiflexible cyclic and linear chains moderately and strongly confined in nanochannels. In Macromolecules, 2012, vol. 45, p. 2597 - 2608. (5.167 - IF2011). (2012 - Current Contents). ISSN 0024-9297. Typ: ADCA
  2. BENKOVÁ, Zuzana - CORDEIRO, M. Natália D. S. Molecular dynamics study of poly(ethylene oxide) chains densely grafted on siloxane surface in dry conditions. In Journal of Physical Chemistry C, 2012, vol. 116, p. 5576 - 3584. (4.805 - IF2011). (2012 - Current Contents). ISSN 1932-7447. Typ: ADCA
  3. CIFRA, Peter - BLEHA, Tomáš. Detection of chain backfolding in simulation of DNA in nanofluidic channels. In SOFT MATTER, 2012, vol. 8, p. 9022 - 9028. (4.390 - IF2011). (2012 - Current Contents). ISSN 1744-683X. Typ: ADCA
  4. CIFRA, Peter - BLEHA, Tomáš. Free energy of polymers confined in open and closed cavities. In Macromolecular Theory and Simulations, 2012, vol. 21, p. 15 - 23. (1.709 - IF2011). (2012 - Current Contents). ISSN 1022-1344. Typ: ADCA
  5. CIFRA, Peter. Weak -to-strong confinement transition of semi-flexible macromolecules in slit and in channel. In Journal of Chemical Physics, 2012, vol. 136, art.no.024902. (3.333 - IF2011). (2012 - Current Contents). ISSN 0021-9606. Typ: ADCA
  6. REITH, Daniel - CIFRA, Peter - STASIAK, Andrzej - VIRNAU, Peter. Effective stiffening of DNA due to nematic ordering causes DNA molecules packed in phage capsids to preferentially form torus knots. In Nucleic acids research, 2012, vol. 40, iss. 11, p. 5129-5137. (8.026 - IF2011). (2012 - Current Contents). ISSN 0305-1048. Typ: ADCA

Publications 2011

ADCA Scientific papers in foreign journals registered in Current Contents Connect with IF (impacted)
  1. BENKOVÁ, Zuzana - CIFRA, Peter. Stiffening transition in semiflexible cyclic macromolecules. In Macromolecular Theory and Simulations, 2011, vol. 20, p. 65 - 74. (1.440 - IF2010). (2011 - Current Contents). ISSN 1022-1344. Typ: ADCA
  2. BENKOVÁ, Zuzana - CORDEIRO, M. Natália D. S. Molecular dynamics study of water interacting with siloxane surface modified by poly(ethylene oxide) chains. In Journal of Physical Chemistry C, 2011, vol. 115, p. 18740 - 18751. (4.524 - IF2010). (2011 - Current Contents). ISSN 1932-7447. Typ: ADCA
  3. BENKOVÁ, Zuzana - SZEFCZYK, Borys - CORDEIRO, M. Natália D. S. Molecular dynamics study of hydrated poly(ethylene oxide) chains grafted on siloxane surface. In Macromolecules, 2011, vol. 44, p. 3639 - 3648. (4.838 - IF2010). (2011 - Current Contents). ISSN 0024-9297. Typ: ADCA
  4. KRUPA, Igor - NEDELČEV, Tomáš - CHORVÁT, Dušan - RAČKO, Dušan - LACÍK, Igor. Glucose diffusivity and porosity in silica hydrogel based on organofunctional silanes. In European Polymer Journal, 2011, vol. 47, p. 1477 - 1484. (2.517 - IF2010). (2011 - Current Contents). ISSN 0014-3057. Typ: ADCA
  5. LINSE, Per - PALENČÁR, Peter - BLEHA, Tomáš. A new two-state polymer folding model and its application to alfa-helical polyalanine. In Journal of physical chemistry B.Materials, surfaces, interfaces, and biophysical, 2011, vol. 115, p. 11448 - 11454. (3.603 - IF2010). (2011 - Current Contents, WOS, SCOPUS). ISSN 1520-6106. Typ: ADCA
  6. PALENČÁR, Peter - BLEHA, Tomáš. Molecular dynamics simulations of the folding of poly (alanine) peptides. In Journal of molecular modeling, 2011, vol. 17, p. 2367 - 2374. (1.871 - IF2010). (2011 - Current Contents). ISSN 1610-2940. Typ: ADCA
  7. RAČKO, Dušan - CAPPONI, S. - ALVAREZ, F. - COLMENERO, J. The free volume of poly(vinyl methylether) as computed in a wide temperature range and at length scales up to the nanoregion. In Journal of Chemical Physics, 2011, vol. 134, iss. 4, art.no. 044512 p.1-14. (2.921 - IF2010). (2011 - Current Contents). ISSN 0021-9606. Typ: ADCA

Publications 2010

ADCA Scientific papers in foreign journals registered in Current Contents Connect with IF (impacted)
  1. CIFRA, Peter - BENKOVÁ, Zuzana - BLEHA, Tomáš. Persistence lenght of DNA molecules confined in nanochannels. In Physical Chemistry Chemical Physics, 2010, vol.12, p. 8934 - 8942. (4.116 - IF2009). (2010 - Current Contents). ISSN 1463-9076. Typ: ADCA
  2. CIFRA, Peter - BLEHA, Tomáš. Shape transition of semi-flexible macromolecules confined in channel and cavity. In European Physical Journal E : Soft Matter and Biological Physics, 2010, vol. 032, p. 273 - 279. (2.019 - IF2009). (2010 - Current Contents). ISSN 1292-8941. Typ: ADCA
  3. KRUPA, Igor - NEDELČEV, Tomáš - RAČKO, Dušan - LACÍK, Igor. Mechanical properties of silica hydrogels prepared and aged at physiological conditions: testing in the compression mode. In Journal of Sol-Gel Science and Technology, 2010, vol. 53, no.1, p. 107 - 114. (1.393 - IF2009). (2010 - Current Contents). ISSN 0928-0707. Typ: ADCA
  4. PALENČÁR, Peter - BLEHA, Tomáš. Folding of polyalanine into helical hairpins. In Macromolecular Theory and Simulations, 2010, vol. 19, p. 488 - 495. (1.683 - IF2009). (2010 - Current Contents). ISSN 1022-1344. Typ: ADCA
ADCB Scientific papers in foreign journals registered in Current Contents Connect without IF (non-impacted)
  1. CIFRA, Peter - BLEHA, Tomáš. Simulation of chain organization in encapsulated polymers. In Macromolecular Symposia, 2010, vol. 296, p. 336 - 341. ISSN 1022-1360. Typ: ADCB